After reviewing this thread, I've realized that one of the reasons for clone believing TaT to be a flawed application is likely based on a misunderstanding of where thermal measurements come from in a PC. This is actually a very, very common problem that needs further explanation.
you also mentioned and issue with cooling, the only issue was with TaT, I've been running the latest Core Temp app showing a 20c lower temp for the cpu's and they've yet to exceed 51c even under synthetic load since.
The most likely explanation for this observation isn't technically a difference in measurement. It's simply a difference in where that temperature is being read from, or what stored value that measurement is being computed against.
You can get CPU temperatures from two places these days. You can either get them from analog diode on the motherboard near the CPU that's intepreted by the BIOS, or you can get them from the DTS (digital thermal sensor) that's on the die of the processor.
If these programs got the CPU temperature from differing places than obviously the values could be different without anything being wrong with either program. Not only is the diode on the motherboard not actually on the CPU, but the temperature provided comes from differing circuitry measured by differing algorithms in the BIOS. In your particular case, however, both of those programs get it from the DTS by reading a MSR (machine-specific register) on the processor.
But this means we run into a different problem, which is what stored value that measurement is being computed against. What you read from the MSR in Intel's DTS isn't actually a temperature. It's a counter that counts down to TjMax (or Tjunction). This value isn't explicitly stored. The published TjMax for mobile Core2s is 85c. The TjMax for desktop processors is not published and differs between cores and maybe even steppings, but for conroes it's widely speculated (and confirmed by experiment) to be 105c.
This immediately explains the 20c difference. You calculate temperature by subtracting the DTS counter from TjMax. Intel's TaT (thermal analysis tool) gives you the 20c higher core temp because it's using the 85c TjMax value. This is because TaT is intended for use on mobile processors even though the processor in this case is really a conroe with a real TjMax of 105. Core Temp gives you the lower (and correct) core temp because it's using the appropriate TjMax for your processor.
So TaT really isn't at fault. It's reading the exact same MSR as CoreTemp, the only issue is that it is applying the wrong TjMax to it. The lesson here is to try and understand what your tools are doing before dismissing them as flawed because their results appear to be inaccurate. TaT is designed for mobile processors, not desktop ones. This is why it will identify any desktop processor as a Pentium M. Using the right tool for the job is essential, and when using a tool that's not specifically designed for the job it's essentially that you understand what it's doing so that the result is correctly undertood.